7 answers

Support for VCF files was added with version 1.1.0 of GenomeBrowse. Single sample VCFs, multi-sample VCFs and even "site"-based VCFs with no sample data are now supported. SNVs and InDels are supported and we will do our best to draw Structural Variants, but their representation in VCF format is less standardized.

We incorporated a new rendering mode for multi-sample "Variant Maps", as well as auto-compression/indexing of VCF to Bgzip/Tabix format required to read files directly for rendering.

Currently any VCF file loaded into GenomeBrowse must be sorted.

Please update to the most recent version of GenomeBrowse to access all available features. To update GenomeBrowse please download the installer from our website.

I am sorry you are having issues loading your BAM and VCF files into GenomeBrowse.

Have you tried loading them through the Add dialog by navigating to their saved location? Our records indicate that you are using the Win64 version, if that is correct there is a know bug in that version for visualizing BAM files which may be causing the issue.

Thank you for your question. We are still in the process of developing and implementing the functionality to load VCF files directly into GenomeBrowse, unfortunately the target date of completion has been pushed to after the first of the year.

For the moment we recommend using our analysis software SVS to create custom annotation tracks from the data within the VCF files that can then be viewed within GenomeBrowse. SVS produces IDF files when creating custom tracks that will be auto-detected by GenomeBrowse.

SVS is Golden Helix’s analysis product for a variety of workflows and is a commercial tool, you can request an evaluation of the software from our evaluation request form.

Please feel free to use SVS in trial mode to curate your custom tracks for use with GenomeBrowse.

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.